1
|
Shaheen N, Qureshi NA, Qureshi MZ, Fatima H, Afzal M, Alhewairini SS. Molecular epidemiological survey of cutaneous leishmaniasis from Azad Jammu and Kashmir, Pakistan. Acta Trop 2020; 206:105434. [PMID: 32126210 DOI: 10.1016/j.actatropica.2020.105434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/24/2020] [Accepted: 02/28/2020] [Indexed: 12/30/2022]
Abstract
Cutaneous leishmaniasis (CL) is an emerging neglected tropical disease in Azad Jammu and Kashmir which is an underdeveloped area. Prevalence and parasite species identification are the key factors to control disease in a particular population, which were the objectives of the present study. Due to a lack of previous data, we performed a district-based active CL surveillance in 2018. The data of CL, suspected (n = 20,000) cases were analyzed statistically and identified the parasite species in microscopic positive cases by ITS1-PCR RFLP and also obtained accession numbers MN891719-28 from gene Bank. The phylogenetic tree was constructed using MEGA6 software. Out of 20,000 CL, suspected cases the highest rate of 4.02% (135/3360) of CL in Mirpur and the lowest 1.58% (8/505) in Neelum was reported. The slide positivity rate, annual parasite incidence rate and annual blood examination rate were 2.27 per 1000 population, 0.08 and 0.34%. The males were more infected 58.12% (297/511) than females 41.88% (214/511) and the age group of 1-20 years were found highly infected 82.78% (423/511) than 21-40 years 13.89% (71/511) and 41-60 years 3.33% (17/511) in the studied population. The patients 56.36% (288/511) had a single lesion whereas 29.35% (150/511) had two, only 10.76% (31/288) and 8% (12/150) were using bed nets. The patients 14.29% (73/511) had three or more lesions were not using bed nets. Only 27.98% (143/511) patients had received treatment, while 72.02% (368/511) didn't. Microscopically positive cases were found to be 2.56% (511/20,000) and ITS1-PCR positive cases were found to be 91.39% (467/511). The RFLP assay confirmed the presence of Leishmania tropica in 467 samples.
Collapse
Affiliation(s)
- Nargis Shaheen
- Department of Zoology, Faculty of Biological Science, Quaid-i-Azam University Islamabad 45320, Pakistan
| | - Naveeda Akhter Qureshi
- Department of Zoology, Faculty of Biological Science, Quaid-i-Azam University Islamabad 45320, Pakistan.
| | | | - Huma Fatima
- Department of Zoology, Faculty of Biological Science, Quaid-i-Azam University Islamabad 45320, Pakistan
| | - Muhammad Afzal
- Department of Zoology, Faculty of Biological Science, Quaid-i-Azam University Islamabad 45320, Pakistan
| | - Saleh S Alhewairini
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Saudi Arabia
| |
Collapse
|
2
|
Yang L, Chen Y, Yu C, Shen B. Biobanks and Their Clinical Application and Informatics Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 939:241-257. [PMID: 27807750 DOI: 10.1007/978-981-10-1503-8_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Biobanks are one of the most important biomedical research resources and contribute to the development of biomarker detection, molecular diagnosis, translational medicine, and multidisciplinary disease research, as well as studies of interactions between genetic and environmental or lifestyle factors. Aiming for the wide clinical application of biobanks, biobanking efforts have recently switched from a focus on accumulating samples to both formalizing and sustaining collections in light of the rapid progress in the fields of personalized medicine and bioinformatics analysis. With the emergence of novel molecular diagnostic technologies, although the bioinformatics platform of biobanks ensures reliable bioinformatics analysis of patient samples, there are a series of challenges facing biobanks in terms of the overall harmonization of policies, integrated processes, and local informatics solutions across the network. Further, there is a controversy regarding the increased role of ethical boards, governance, and accreditation bodies in ensuring that collected samples have sufficient informatics capabilities to be used in biobanks. In this volume, we present a selection of current issues on the inevitable challenges of the clinical application of biobanks in informatics.
Collapse
Affiliation(s)
- Lan Yang
- Center for Systems Biology, Soochow University, No. 1 Shizi Street, 206, 215006, Suzhou, Jiangsu, China
| | - Yalan Chen
- Center for Systems Biology, Soochow University, No. 1 Shizi Street, 206, 215006, Suzhou, Jiangsu, China.,Department of Medical Informatics, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Chunjiang Yu
- Suzhou Industrial Park Institute of Services Outsourcing, No. 99 Ruoshui Road, Suzhou Industrial Park, Suzhou, 215123, Jiangsu, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, No. 1 Shizi Street, 206, 215006, Suzhou, Jiangsu, China.
| |
Collapse
|
3
|
Zhang X, Marjani SL, Hu Z, Weissman SM, Pan X, Wu S. Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects. Cancer Res 2016; 76:1305-12. [PMID: 26941284 DOI: 10.1158/0008-5472.can-15-1907] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/22/2015] [Indexed: 11/16/2022]
Abstract
Advances in genomic technology have enabled the faithful detection and measurement of mutations and the gene expression profile of cancer cells at the single-cell level. Recently, several single-cell sequencing methods have been developed that permit the comprehensive and precise analysis of the cancer-cell genome, transcriptome, and epigenome. The use of these methods to analyze cancer cells has led to a series of unanticipated discoveries, such as the high heterogeneity and stochastic changes in cancer-cell populations, the new driver mutations and the complicated clonal evolution mechanisms, and the novel identification of biomarkers of variant tumors. These methods and the knowledge gained from their utilization could potentially improve the early detection and monitoring of rare cancer cells, such as circulating tumor cells and disseminated tumor cells, and promote the development of personalized and highly precise cancer therapy. Here, we discuss the current methods for single cancer-cell sequencing, with a strong focus on those practically used or potentially valuable in cancer research, including single-cell isolation, whole genome and transcriptome amplification, epigenome profiling, multi-dimensional sequencing, and next-generation sequencing and analysis. We also examine the current applications, challenges, and prospects of single cancer-cell sequencing.
Collapse
Affiliation(s)
- Xiaoyan Zhang
- Hangzhou Cancer Institution, Hangzhou Cancer Hospital, Hangzhou, Zhejiang Province, P. R. China
| | - Sadie L Marjani
- Department of Biology, Central Connecticut State University, New Britain, Connecticut
| | - Zhaoyang Hu
- Hangzhou Cancer Institution, Hangzhou Cancer Hospital, Hangzhou, Zhejiang Province, P. R. China
| | - Sherman M Weissman
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Xinghua Pan
- Hangzhou Cancer Institution, Hangzhou Cancer Hospital, Hangzhou, Zhejiang Province, P. R. China. Department of Genetics, Yale University School of Medicine, New Haven, Connecticut. Department of Biochemistry, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, P.R. China.
| | - Shixiu Wu
- Hangzhou Cancer Institution, Hangzhou Cancer Hospital, Hangzhou, Zhejiang Province, P. R. China.
| |
Collapse
|
4
|
Foitzik M, Stumpp SN, Grischke J, Eberhard J, Stiesch M. Evaluation of FTA ® paper for storage of oral meta-genomic DNA. Biopreserv Biobank 2015; 12:337-42. [PMID: 25340943 DOI: 10.1089/bio.2014.0027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIM The purpose of the present study was to evaluate the short-term storage of meta-genomic DNA from native oral biofilms on FTA(®) paper. MATERIALS AND METHODS Thirteen volunteers of both sexes received an acrylic splint for intraoral biofilm formation over a period of 48 hours. The biofilms were collected, resuspended in phosphate-buffered saline, and either stored on FTA(®) paper or directly processed by standard laboratory DNA extraction. The nucleic acid extraction efficiencies were evaluated by 16S rDNA targeted SSCP fingerprinting. The acquired banding pattern of FTA-derived meta-genomic DNA was compared to a standard DNA preparation protocol. Sensitivity and positive predictive values were calculated. RESULTS The volunteers showed inter-individual differences in their bacterial species composition. A total of 200 bands were found for both methods and 85% of the banding patterns were equal, representing a sensitivity of 0.941 and a false-negative predictive value of 0.059. CONCLUSION Meta-genomic DNA sampling, extraction, and adhesion using FTA(®) paper is a reliable method for storage of microbial DNA for a short period of time.
Collapse
Affiliation(s)
- Magdalena Foitzik
- Department of Prosthetic Denstiry and Biomedical Materials Science, Hannover Medical School , Hannover, Germany
| | | | | | | | | |
Collapse
|
5
|
Sørensen KM. Whole Genome Amplification from Blood Spot Samples. Methods Mol Biol 2015; 1347:163-178. [PMID: 26374317 DOI: 10.1007/978-1-4939-2990-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Whole genome amplification is an invaluable technique when working with DNA extracted from blood spots, as the DNA obtained from this source often is too limited for extensive genetic analysis. Two techniques that amplify the entire genome are common. Here, both are described with focus on the benefits and drawbacks of each system. However, in order to obtain the best possible WGA result the quality of input DNA extracted from the blood spot is essential, but also time consumption, flexibility in format and elution volume and price of the technology are factors influencing system choice. Here, three DNA extraction techniques are described and the above aspects are compared between the systems.
Collapse
Affiliation(s)
- Karina Meden Sørensen
- The Danish National Biobank, Statens Serum Institut, Artillerivej 5, Copenhagen, 2300, Danmark.
| |
Collapse
|
6
|
Boeckhout M, Douglas CM. Governing the research-care divide in clinical biobanking: Dutch perspectives. LIFE SCIENCES, SOCIETY AND POLICY 2015; 11:7. [PMID: 26246123 PMCID: PMC4551681 DOI: 10.1186/s40504-015-0025-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 07/03/2015] [Indexed: 05/18/2023]
Abstract
Biobanking, the large-scale, systematic collection of data and tissue for open-ended research purposes, is on the rise, particularly in clinical research. The infrastructures for the systematic procurement, management and eventual use of human tissue and data are positioned between healthcare and research. However, the positioning of biobanking infrastructures and transfer of tissue and data between research and care is not an innocuous go-between. Instead, it involves changes in both domains and raises issues about how distinctions between research and care are drawn and policed. Based on an analysis of the emergence and development of clinical biobanking in the Netherlands, this article explores how processes of bio-objectification associated with biobanking arise, redefining the ways in which distinctions between research and clinical care are governed.
Collapse
Affiliation(s)
- Martin Boeckhout
- />BBMRI-NL, Department of Human Genetics, Leiden University Medical Centre, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Conor M.W. Douglas
- />Faculty of Pharmaceutical Sciences, Collaboration for Outcomes Research and Evaluation (CORE), The University of British Columbia Vancouver Campus, 4103A-2405 Wesbrook Mall, Vancouver, BC V6T 1Z3 Canada
| |
Collapse
|
7
|
Sirdah MM. Superparamagnetic-bead Based Method: An Effective DNA Extraction from Dried Blood Spots (DBS) for Diagnostic PCR. J Clin Diagn Res 2014; 8:FC01-4. [PMID: 24959449 DOI: 10.7860/jcdr/2014/8171.4226] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 03/27/2014] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Storing blood as dried spots on filter paper is a trustworthy approach used in genetic screening issues which justifies the necessity for a reliable DNA extraction method. The present work aims to investigate the effectiveness of superparamagnetic-bead based method in extracting DNA from dried blood spots (DBS). MATERIALS AND METHODS Sixteen venous blood samples collected in K3-EDTA tubes (400μl of whole blood) were used for the spotting (4 circles each 100μl) on Ahlstrom 226 grad filter papers, for extraction and comparison. To ensure effectiveness, the extracted DNA was checked for quantity using the Quant-iT™ dsDNA Broad-Range Assay Kit and for quality by polymerase chain reaction (PCR) amplification of 344 bp segment of the HBB gene. Hybridization assays based on the dynamic allele specific hybridization (DASH) technique for two hemoglobin beta (HBB) mutations in genomic DNA extracted from DBS of ß-thalassemia patients were also performed to ensure the quality of extraction. RESULTS The results revealed a compatible effectiveness of the superparamagnetic-bead based method in extracting DNA from DBS particularly when incubating the DBS with lysis buffers BL+BLM overnight. A mean concentration of 21ng/ μl was obtained with lysis buffers BL+BLM overnight incubation compared to 5.2 ng/μl for 2 h incubation with lysis buffers BL+BLM and 4.7 ng/μl when extraction performed using the lysis buffer BLM alone. Moreover, PCR amplification of 344 bp segment of the HBB showed a good quality of the extracted DNA. CONCLUSION It was concluded that the superparamagnetic-bead based method is a reliable and effective method for DNA extraction from DBS and can be adopted for genetic diagnostic purposes.
Collapse
|
8
|
St. Julien KR, Jelliffe-Pawlowski LL, Shaw GM, Stevenson DK, O’Brodovich HM, Krasnow MA. High quality genome-wide genotyping from archived dried blood spots without DNA amplification. PLoS One 2013; 8:e64710. [PMID: 23737996 PMCID: PMC3667813 DOI: 10.1371/journal.pone.0064710] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 04/17/2013] [Indexed: 11/19/2022] Open
Abstract
Spots of blood are routinely collected from newborn babies onto filter paper called Guthrie cards and used to screen for metabolic and genetic disorders. The archived dried blood spots are an important and precious resource for genomic research. Whole genome amplification of dried blood spot DNA has been used to provide DNA for genome-wide SNP genotyping. Here we describe a 96 well format procedure to extract DNA from a portion of a dried blood spot that provides sufficient unamplified genomic DNA for genome-wide single nucleotide polymorphism (SNP) genotyping. We show that SNP genotyping of the unamplified DNA is more robust than genotyping amplified dried blood spot DNA, is comparable in cost, and can be done with thousands of samples. This procedure can be used for genome-wide association studies and other large-scale genomic analyses that require robust, high-accuracy genotyping of dried blood spot DNA.
Collapse
Affiliation(s)
- Krystal R. St. Julien
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Laura L. Jelliffe-Pawlowski
- California Genetic Disease Screening Program of the California Department of Public Health, Richmond, California, United States of America
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - David K. Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Hugh M. O’Brodovich
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Mark A. Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| | | |
Collapse
|
9
|
Klassen TL, Drabek J, Tomson T, Sveinsson O, von Döbeln U, Noebels JL, Goldman AM. Visual automated fluorescence electrophoresis provides simultaneous quality, quantity, and molecular weight spectra for genomic DNA from archived neonatal blood spots. J Mol Diagn 2013; 15:283-90. [PMID: 23518217 DOI: 10.1016/j.jmoldx.2013.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/15/2013] [Accepted: 01/23/2013] [Indexed: 01/26/2023] Open
Abstract
The Guthrie 903 card archived dried blood spots (DBSs) are a unique but terminal resource amenable for individual and population-wide genomic profiling. The limited amounts of DBS-derived genomic DNA (gDNA) can be whole genome amplified, producing sufficient gDNA for genomic applications, albeit with variable success; optimizing the isolation of high-quality DNA from these finite, low-yield specimens is essential. Agarose gel electrophoresis and spectrophotometry are established postextraction quality control (QC) methods but lack the power to disclose detailed structural, qualitative, or quantitative aspects that underlie gDNA failure in downstream applications. Visual automated fluorescence electrophoresis (VAFE) is a novel QC technology that affords precise quality, quantity, and molecular weight of double-stranded DNA from a single microliter of sample. We extracted DNA from 3-mm DBSs archived in the Swedish Neonatal Repository for >30 years and performed the first quantitative and qualitative analyses of DBS-derived DNA on VAFE, before and after whole genome amplified, in parallel with traditional QC methods. The VAFE QC data were correlated with subsequent sample performance in PCR, sequencing, and high-density comparative genome hybridization array. We observed improved standardization of nucleic acid quantity, quality and integrity, and high performance in the downstream genomic technologies. Addition of VAFE measures in QC increases confidence in the validity of genetic data and allows cost-effective downstream analysis of gDNA for investigational and diagnostic applications.
Collapse
Affiliation(s)
- Tara L Klassen
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA.
| | | | | | | | | | | | | |
Collapse
|
10
|
Lee JCI, Tsai LC, Lai PY, Lee CC, Lin CY, Huang TY, Linacre A, Hsieh HM. Evaluating the performance of whole genome amplification for use in low template DNA typing. MEDICINE, SCIENCE, AND THE LAW 2012; 52:223-228. [PMID: 22875794 DOI: 10.1258/msl.2012.011126] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report on the performance of two whole genome amplification methods, GenomiPhi™ amplification and modified-improved primer extension preamplification (mIPEP), when analysing low template DNA samples. Template as low as 10 pg treated with mIPEP generated more than 1 ng of DNA that could be used in STR typing. Initial templates of 100-10 pg, when treated with mIPEP, generated an increase in alleles compared with control samples. Partial profiles using the AmpFℓSTR(®) Identifiler™ Kit were produced from this suboptimal DNA template, with 70% of the possible alleles (21.7 ± 2.1 in 32 alleles) recorded, using the mIPEP amplified products with an initial template of 100 pg. Allelic imbalance decreased with samples treated with whole genome amplification method (WGA) compared with those without this initial treatment. Further methods for improvement were also analysed including altering the condition of electrokinetic injection, and the successful DNA typing rate was increased to about 80%. This report illustrates the potential use and limitations of WGA for low template samples.
Collapse
Affiliation(s)
- James Chun-I Lee
- Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Cryptic parasite revealed improved prospects for treatment and control of human cryptosporidiosis through advanced technologies. ADVANCES IN PARASITOLOGY 2012; 77:141-73. [PMID: 22137584 DOI: 10.1016/b978-0-12-391429-3.00007-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cryptosporidium is an important genus of parasitic protozoa of humans and other vertebrates and is a major cause of intestinal disease globally. Unlike many common causes of infectious enteritis, there are no widely available, effective vaccine or drug-based intervention strategies for Cryptosporidium, and control is focused mainly on prevention. This approach is particularly deficient for infections of severely immunocompromised and/or suppressed, the elderly or malnourished people. However, cryptosporidiosis also presents a significant burden on immunocompetent individuals, and can, for example have lasting effects on the physical and mental development of children infected at an early age. In the last few decades, our understanding of Cryptosporidium has expanded significantly in numerous areas, including the parasite life-cycle, the processes of excystation, cellular invasion and reproduction, and the interplay between parasite and host. Nonetheless, despite extensive research, many aspects of the biology of Cryptosporidium remain unknown, and treatment and control are challenging. Here, we review the current state of knowledge of Cryptosporidium, with a focus on major advances arising from the recently completed genome sequences of the two species of greatest relevance in humans, namely Cryptosporidium hominis and Cryptosporidium parvum. In addition, we discuss the potential of next-generation sequencing technologies, new advances in in silico analyses and progress in in vitro culturing systems to bridge these gaps and to lead toward effective treatment and control of cryptosporidiosis.
Collapse
|
12
|
Demontis D, Nyegaard M, Buttenschøn HN, Hedemand A, Pedersen CB, Grove J, Flint TJ, Nordentoft M, Werge T, Hougaard DM, Sørensen KM, Yolken RH, Mors O, Børglum AD, Mortensen PB. Association of GRIN1 and GRIN2A-D with schizophrenia and genetic interaction with maternal herpes simplex virus-2 infection affecting disease risk. Am J Med Genet B Neuropsychiatr Genet 2011; 156B:913-22. [PMID: 21919190 DOI: 10.1002/ajmg.b.31234] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 08/04/2011] [Indexed: 02/05/2023]
Abstract
N-methyl-D-aspartate (NMDA) receptors are very important for proper brain development and several lines of evidence support that hypofunction of the NMDA receptors are involved in the pathophysiology of schizophrenia. Gene variation and gene-environmental interactions involving the genes encoding the NMDA receptors are therefore likely to influence the risk of schizophrenia. The aim of this study was to determine (1) whether SNP variation in the genes (GRIN1, GRIN2A, GRIN2B, GRIN2C, and GRIN2D) encoding the NMDA receptor were associated with schizophrenia; (2) whether GRIN gene variation in the offspring interacted with maternal herpes simplex virus-2 (HSV-2) seropositivity during pregnancy influencing the risk of schizophrenia later in life. Individuals from three independently collected Danish case control samples were genotyped for 81 tagSNPs (in total 984 individuals diagnosed with schizophrenia and 1,500 control persons) and antibodies against maternal HSV-2 infection were measured in one of the samples (365 cases and 365 controls). Nine SNPs out of 30 in GRIN2B were significantly associated with schizophrenia. One SNP remained significant after Bonferroni correction (rs1806194, P(nominal) = 0.0008). Significant interaction between maternal HSV-2 seropositivity and GRIN2B genetic variation in the offspring were observed for seven SNPs and two remained significant after Bonferroni correction (rs1805539, P(nominal) = 0.0001 and rs1806205, P(nominal) = 0.0008). The significant associations and interactions were located at the 3' region of GRIN2B suggesting that genetic variation in this part of the gene may be involved in the pathophysiology of schizophrenia.
Collapse
Affiliation(s)
- Ditte Demontis
- Department of Human Genetics, Aarhus University, Aarhus, Denmark.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Glimelius I, Rubin J, Rostgaard K, Amini RM, Simonsson M, Sorensen KM, Smedby KE, Venge P, Hjalgrim H, Molin D, Enblad G. Predictors of histology, tissue eosinophilia and mast cell infiltration in Hodgkin's lymphoma--a population-based study. Eur J Haematol 2011; 87:208-16. [PMID: 21623917 DOI: 10.1111/j.1600-0609.2011.01652.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Classical Hodgkin's lymphoma (HL) lesions comprise few tumour cells, surrounded by numerous inflammatory cells. Like in other malignancies, the microenvironment is presumed to be clinically important in HL; however, microenvironment predictors remain poorly characterised. The aim of this study was to investigate how selected patient characteristics and genetic factors affect HL phenotype, in particular tissue eosinophilia, mast cell counts and HL histological subtype. METHODS In a population-based study, patients with HL were interviewed about potential HL risk factors. Available tumours, n=448, were classified histologically; the number of eosinophils and mast cells were estimated, and eosinophil cationic protein (ECP) and eosinophil protein-x (EPX) gene polymorphisms were determined. Associations were assessed in regression models. RESULTS Self-reported history of asthma was predictive of having tumour eosinophilia [≥200 eosinophils/10 high power fields, univariate odds ratio (OR)=2.22, 95% CI 1.06-4.64, P=0.03]. High numbers of eosinophils were predominantly seen in patients carrying the genotype ECP434GG [multivariate relative levels (RLs)=1.84, 95% CI 1.02-3.30, P=0.04]. Lower number of eosinophils was seen in Epstein-Barr virus (EBV)-positive tumours (univariate RL=0.52, 95% CI 0.3-0.9, P=0.02) and in older patients (univariate RL=0.85, 95% CI 0.73-0.99, P=0.03). Well-known factors such as young age, female sex and EBV-negative status predicted nodular sclerosis histology. CONCLUSION The number of eosinophils in HL tumours is influenced by patient traits such as asthma, ECP genotype and EBV status. EBV status was predictive of histology.
Collapse
Affiliation(s)
- Ingrid Glimelius
- Department of Radiology, Oncology and Radiation Science Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Parker JK, Chang TY, Meschke JS. Amplification of viral RNA from drinking water using TransPlex™ whole-transcriptome amplification. J Appl Microbiol 2011; 111:216-23. [PMID: 21477067 PMCID: PMC7197749 DOI: 10.1111/j.1365-2672.2011.05029.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aims: Viral pathogens in environmental media are generally highly diffuse, yet small quantities of pathogens may pose a health risk. This study evaluates the ability of TransPlex™ whole transcriptome amplification (WTA) to amplify small quantities of RNA viruses from complex environmental matrices containing background nucleic acids. Methods and Results: DNA extracts from mock drinking water samples containing mixed microbial populations were spiked with small quantities of echovirus type 13 (EV) RNA. Samples were amplified using a Transplex™ WTA kit, and EV‐specific quantitative reverse transcription polymerase chain reaction (qRT‐PCR) was used to quantify target pathogens before and after application of WTA. Samples amplified by WTA demonstrated a decreased limit of detection. The log‐linear relationship between serial dilutions was maintained following amplification by WTA. Conclusions: WTA is able to increase the quantity of target organism RNA in mixed populations, while maintaining log linearity of amplification across different target concentrations. Significance and Impact of the Study: WTA may serve as an effective preamplification step to increase the levels of RNA prior to detection by other molecular methods such as PCR, microarrays and sequencing.
Collapse
Affiliation(s)
- J K Parker
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | | | | |
Collapse
|
15
|
Enciso-Mora V, Broderick P, Ma Y, Jarrett RF, Hjalgrim H, Hemminki K, van den Berg A, Olver B, Lloyd A, Dobbins SE, Lightfoot T, van Leeuwen FE, Försti A, Diepstra A, Broeks A, Vijayakrishnan J, Shield L, Lake A, Montgomery D, Roman E, Engert A, von Strandmann EP, Reiners KS, Nolte IM, Smedby KE, Adami HO, Russell NS, Glimelius B, Hamilton-Dutoit S, de Bruin M, Ryder LP, Molin D, Sorensen KM, Chang ET, Taylor M, Cooke R, Hofstra R, Westers H, van Wezel T, van Eijk R, Ashworth A, Rostgaard K, Melbye M, Swerdlow AJ, Houlston RS. A genome-wide association study of Hodgkin's lymphoma identifies new susceptibility loci at 2p16.1 (REL), 8q24.21 and 10p14 (GATA3). Nat Genet 2010; 42:1126-1130. [PMID: 21037568 PMCID: PMC4268499 DOI: 10.1038/ng.696] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/30/2010] [Indexed: 12/14/2022]
Abstract
To identify susceptibility loci for classical Hodgkin's lymphoma (cHL), we conducted a genome-wide association study of 589 individuals with cHL (cases) and 5,199 controls with validation in four independent samples totaling 2,057 cases and 3,416 controls. We identified three new susceptibility loci at 2p16.1 (rs1432295, REL, odds ratio (OR) = 1.22, combined P = 1.91 × 10(-8)), 8q24.21 (rs2019960, PVT1, OR = 1.33, combined P = 1.26 × 10(-13)) and 10p14 (rs501764, GATA3, OR = 1.25, combined P = 7.05 × 10(-8)). Furthermore, we confirmed the role of the major histocompatibility complex in disease etiology by revealing a strong human leukocyte antigen (HLA) association (rs6903608, OR = 1.70, combined P = 2.84 × 10(-50)). These data provide new insight into the pathogenesis of cHL.
Collapse
MESH Headings
- Adult
- Chromosomes, Human/genetics
- Chromosomes, Human, Pair 10/genetics
- Chromosomes, Human, Pair 2/genetics
- Chromosomes, Human, Pair 8/genetics
- Female
- GATA3 Transcription Factor/genetics
- Genetic Loci/genetics
- Genetic Predisposition to Disease
- Genome, Human/genetics
- Genome-Wide Association Study
- Hodgkin Disease/genetics
- Humans
- Male
- Polymorphism, Single Nucleotide/genetics
- Proto-Oncogene Proteins c-rel/genetics
- Recombination, Genetic
Collapse
Affiliation(s)
- Victor Enciso-Mora
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Peter Broderick
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Yussanne Ma
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Ruth F Jarrett
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany and Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden
| | - Anke van den Berg
- Department of Pathology & Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Bianca Olver
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Amy Lloyd
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Sara E Dobbins
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Tracy Lightfoot
- Epidemiology & Genetics Unit, Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Flora E van Leeuwen
- Department of Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany and Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden
| | - Arjan Diepstra
- Department of Pathology & Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Annegien Broeks
- Department of Experimental Therapy, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | - Lesley Shield
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Annette Lake
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Dorothy Montgomery
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Eve Roman
- Epidemiology & Genetics Unit, Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Andreas Engert
- University Hospital of Cologne, Department of Internal Medicine, Cologne, Germany
| | | | - Katrin S. Reiners
- University Hospital of Cologne, Department of Internal Medicine, Cologne, Germany
| | - Ilja M Nolte
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University Medical Centre Groningen, University of Groningen, the Netherlands
| | - Karin E Smedby
- Unit of Clinical Epidemiology, Department of Medicine, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-171 77, Stockholm, Sweden
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Nicola S Russell
- Department of Radiotherapy, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Bengt Glimelius
- Department of Pathology and Oncology, Karolinska Institutet, SE-171 77, Stockholm, Sweden
- Department of Oncology, Radiology and Clinical Immunology, Uppsala University, SE-751 85, Uppsala, Sweden
| | | | - Marieke de Bruin
- Department of Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Lars P Ryder
- Department of Clinical Immunology, University Hospital of Copenhagen, Rigshospitalet, DK-2100, Copenhagen, Denmark
| | - Daniel Molin
- Department of Oncology, Radiology and Clinical Immunology, Uppsala University, Uppsala, Sweden
| | | | - Ellen T Chang
- Cancer Prevention Institute of California, Fremont, CA 94538
- Division of Epidemiology, Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Malcolm Taylor
- Cancer Immunogenetics Group, School of Cancer & Enabling Sciences, University of Manchester, Research Floor, St Mary’s Hospital, Manchester, M13 9WL, UK
| | - Rosie Cooke
- Section of Epidemiology, Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Robert Hofstra
- Department of Genetics University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Helga Westers
- Department of Genetics University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alan Ashworth
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Klaus Rostgaard
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Richard S Houlston
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, SM2 5NG, UK
| |
Collapse
|
16
|
|
17
|
Fernberg P, Chang ET, Duvefelt K, Hjalgrim H, Eloranta S, Sørensen KM, Porwit A, Humphreys K, Melbye M, Ekström Smedby K. Genetic variation in chromosomal translocation breakpoint and immune function genes and risk of non-Hodgkin lymphoma. Cancer Causes Control 2010; 21:759-69. [PMID: 20087644 DOI: 10.1007/s10552-010-9504-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 01/06/2010] [Indexed: 12/19/2022]
Affiliation(s)
- Pia Fernberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Bucasas KL, Pandya GA, Pradhan S, Fleischmann RD, Peterson SN, Belmont JW. Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping. BMC Genet 2009; 10:85. [PMID: 20021669 PMCID: PMC2803178 DOI: 10.1186/1471-2156-10-85] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 12/18/2009] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Whole genome amplification (WGA) offers new possibilities for genome-wide association studies where limited DNA samples have been collected. This study provides a realistic and high-precision assessment of WGA DNA genotyping performance from 20-year old archived serum samples using the Affymetrix Genome-Wide Human SNP Array 6.0 (SNP6.0) platform. RESULTS Whole-genome amplified (WGA) DNA samples from 45 archived serum replicates and 5 fresh sera paired with non-amplified genomic DNA were genotyped in duplicate. All genotyped samples passed the imposed QC thresholds for quantity and quality. In general, WGA serum DNA samples produced low call rates (45.00 +/- 2.69%), although reproducibility for successfully called markers was favorable (concordance = 95.61 +/- 4.39%). Heterozygote dropouts explained the majority (>85% in technical replicates, 50% in paired genomic/serum samples) of discordant results. Genotyping performance on WGA serum DNA samples was improved by implementation of Corrected Robust Linear Model with Maximum Likelihood Classification (CRLMM) algorithm but at the loss of many samples which failed to pass its quality threshold. Poor genotype clustering was evident in the samples that failed the CRLMM confidence threshold. CONCLUSIONS We conclude that while it is possible to extract genomic DNA and subsequently perform whole-genome amplification from archived serum samples, WGA serum DNA did not perform well and appeared unsuitable for high-resolution genotyping on these arrays.
Collapse
Affiliation(s)
- Kristine L Bucasas
- Department of Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gagan A Pandya
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Sonal Pradhan
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Robert D Fleischmann
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Scott N Peterson
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - John W Belmont
- Department of Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
19
|
Hollegaard MV, Thorsen P, Norgaard-Pedersen B, Hougaard DM. Genotyping whole-genome-amplified DNA from 3- to 25-year-old neonatal dried blood spot samples with reference to fresh genomic DNA. Electrophoresis 2009; 30:2532-5. [DOI: 10.1002/elps.200800655] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
20
|
Hardin J, Finnell RH, Wong D, Hogan ME, Horovitz J, Shu J, Shaw GM. Whole genome microarray analysis, from neonatal blood cards. BMC Genet 2009; 10:38. [PMID: 19624846 PMCID: PMC2722673 DOI: 10.1186/1471-2156-10-38] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Accepted: 07/22/2009] [Indexed: 11/24/2022] Open
Abstract
Background Neonatal blood, obtained from a heel stick and stored dry on paper cards, has been the standard for birth defects screening for 50 years. Such dried blood samples are used, primarily, for analysis of small-molecule analytes. More recently, the DNA complement of such dried blood cards has been used for targeted genetic testing, such as for single nucleotide polymorphism in cystic fibrosis. Expansion of such testing to include polygenic traits, and perhaps whole genome scanning, has been discussed as a formal possibility. However, until now the amount of DNA that might be obtained from such dried blood cards has been limiting, due to inefficient DNA recovery technology. Results A new technology is employed for efficient DNA release from a standard neonatal blood card. Using standard Guthrie cards, stored an average of ten years post-collection, about 1/40th of the air-dried neonatal blood specimen (two 3 mm punches) was processed to obtain DNA that was sufficient in mass and quality for direct use in microarray-based whole genome scanning. Using that same DNA release technology, it is also shown that approximately 1/250th of the original purified DNA (about 1 ng) could be subjected to whole genome amplification, thus yielding an additional microgram of amplified DNA product. That amplified DNA product was then used in microarray analysis and yielded statistical concordance of 99% or greater to the primary, unamplified DNA sample. Conclusion Together, these data suggest that DNA obtained from less than 10% of a standard neonatal blood specimen, stored dry for several years on a Guthrie card, can support a program of genome-wide neonatal genetic testing.
Collapse
Affiliation(s)
- Jill Hardin
- University of California Berkeley, School of Public Health, Berkeley, CA 94720, USA.
| | | | | | | | | | | | | |
Collapse
|
21
|
Hollegaard MV, Grauholm J, Børglum A, Nyegaard M, Nørgaard-Pedersen B, Ørntoft T, Mortensen PB, Wiuf C, Mors O, Didriksen M, Thorsen P, Hougaard DM. Genome-wide scans using archived neonatal dried blood spot samples. BMC Genomics 2009; 10:297. [PMID: 19575812 PMCID: PMC2713266 DOI: 10.1186/1471-2164-10-297] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 07/04/2009] [Indexed: 12/01/2022] Open
Abstract
Background Identification of disease susceptible genes requires access to DNA from numerous well-characterised subjects. Archived residual dried blood spot samples from national newborn screening programs may provide DNA from entire populations and medical registries the corresponding clinical information. The amount of DNA available in these samples is however rarely sufficient for reliable genome-wide scans, and whole-genome amplification may thus be necessary. This study assess the quality of DNA obtained from different amplification protocols by evaluating fidelity and robustness of the genotyping of 610,000 single nucleotide polymorphisms, using the Illumina Infinium HD Human610-Quad BeadChip. Whole-genome amplified DNA from 24 neonatal dried blood spot samples stored between 15 to 25 years was tested, and high-quality genomic DNA from 8 of the same individuals was used as reference. Results Using 3.2 mm disks from dried blood spot samples the optimal DNA-extraction and amplification protocol resulted in call-rates between 99.15% – 99.73% (mean 99.56%, N = 16), and conflicts with reference DNA in only three per 10,000 genotype calls. Conclusion Whole-genome amplified DNA from archived neonatal dried blood spot samples can be used for reliable genome-wide scans and is a cost-efficient alternative to collecting new samples.
Collapse
Affiliation(s)
- Mads V Hollegaard
- Section of Neonatal Screening and Hormones, Statens Serum Institut, Copenhagen, Denmark.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Hollegaard MV, Grove J, Thorsen P, Nørgaard-Pedersen B, Hougaard DM. High-Throughput Genotyping on Archived Dried Blood Spot Samples. Genet Test Mol Biomarkers 2009; 13:173-9. [DOI: 10.1089/gtmb.2008.0073] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Mads V. Hollegaard
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Copenhagen, Denmark
- NANEA, Department of Epidemiology, Institute of Public Health, University of Aarhus, Aarhus, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Jakob Grove
- NANEA, Department of Epidemiology, Institute of Public Health, University of Aarhus, Aarhus, Denmark
| | - Poul Thorsen
- NANEA, Department of Epidemiology, Institute of Public Health, University of Aarhus, Aarhus, Denmark
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Bent Nørgaard-Pedersen
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - David M. Hougaard
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
23
|
García-Merino I, de Las Cuevas N, Jiménez JL, Gallego J, Gómez C, Prieto C, Serramía MJ, Lorente R, Muñoz-Fernández MA. The Spanish HIV BioBank: a model of cooperative HIV research. Retrovirology 2009; 6:27. [PMID: 19272145 PMCID: PMC2667474 DOI: 10.1186/1742-4690-6-27] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 03/09/2009] [Indexed: 11/14/2022] Open
Abstract
Background The collection of samples from HIV-infected patients is the beginning of the chain of translational research. To carry out quality research that could eventually end in a personalized treatment for HIV, it is essential to guarantee the availability, quality and traceability of samples, under a strict system of quality management. Methods The Spanish HIV BioBank was created with the objectives of processing, storing and providing distinct samples from HIV/AIDS patients, categorized according to strictly defined characteristics, free of charge to research projects. Strict compliance to ethical norms is always guaranteed. Results At the moment, the HIV BioBank possesses nearly 50,000 vials containing different prospective longitudinal study sample types. More than 1,700 of these samples are now used in 19 national and international research projects. Conclusion The HIV BioBank represents a novel approach to HIV research that might be of general interest not only for basic and clinical research teams working on HIV, but also for those groups trying to establish large networks focused on research on specific clinical problems. It also represents a model to stimulate cooperative research among large numbers of research groups working as a network on specific clinical problems. The main objective of this article is to show the structure and function of the HIV BioBank that allow it to very efficiently release samples to different research project not only in Spain but also in other countries.
Collapse
|
24
|
A population-based association study of glutamate decarboxylase 1 as a candidate gene for autism. J Neural Transm (Vienna) 2009; 116:381-8. [PMID: 19139806 DOI: 10.1007/s00702-008-0142-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 10/06/2008] [Indexed: 10/21/2022]
Abstract
Linkage studies, genome-wide scans and screening of possible candidate genes suggest that chromosome 2q31 may harbour one or more susceptibility genes for autism. The glutamate decarboxylase gene 1 (GAD1) located within chromosome 2q31 encodes the enzyme, GAD67, catalyzing the production of gamma-aminobutyric acid (GABA) from glutamate. Numerous independent findings have suggested the GABAergic system to be involved in autism. The present study investigates a Danish population-based, case-control sample of 444 subjects with childhood autism and 444 controls. Nine single nucleotide polymorphisms (SNPs) comprising the GAD1 gene and the microsatellite marker D2S2381 were examined for association with autism. We found no association between childhood autism and any single marker or 2-5 marker haplotypes. However, a rare nine-marker haplotype was associated with childhood autism. We cannot exclude neither GAD1 as a susceptibility gene nor the possibility of another susceptibility gene for autism to be located on chromosome 2q31.
Collapse
|
25
|
Haak PT, Busik JV, Kort EJ, Tikhonenko M, Paneth N, Resau JH. Archived unfrozen neonatal blood spots are amenable to quantitative gene expression analysis. Neonatology 2009; 95:210-6. [PMID: 18799893 PMCID: PMC2693916 DOI: 10.1159/000155652] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Accepted: 04/22/2008] [Indexed: 01/11/2023]
Abstract
BACKGROUND State laws in the USA mandate that blood be drawn from all newborn infants to screen for health-threatening conditions. These screening assays consume only a small portion of the blood samples, which are collected on filter paper ('Guthrie') cards. Many states archive unused blood spots, often in unrefrigerated storage. OBJECTIVES While individual RNA transcripts have been identified from archived neonatal blood spots, no study to date has performed quantitative analysis of archived blood spot RNA. METHODS We demonstrate that RNA can be isolated and amplified from newborn blood spots stored unfrozen for as long as 9 years, and can be analyzed by microarray and qPCR. RESULTS Microarray assays of archived neonatal blood spots consistently detected 3,000-4,000 expressed genes with correlations of 0.90 between replicates. Blood spot mRNA is amenable to qPCR and we detected biologically relevant expression levels of housekeeping and immune-mediating genes. CONCLUSIONS These experiments demonstrate the feasibility of using blood spots as a source of RNA which can be analyzed using quantitative microarray and qPCR assays. The application of these methods to the analysis of widely collected biological specimens may be a valuable resource for the study of perinatal determinants of disease development.
Collapse
Affiliation(s)
- Peterson T Haak
- Laboratory of Microarray Technology, Van Andel Research Institute, Grand Rapids, Mich. 49503, USA
| | | | | | | | | | | |
Collapse
|
26
|
Maragh S, Jakupciak JP, Wagner PD, Rom WN, Sidransky D, Srivastava S, O'Connell CD. Multiple strand displacement amplification of mitochondrial DNA from clinical samples. BMC MEDICAL GENETICS 2008; 9:7. [PMID: 18257929 PMCID: PMC2268916 DOI: 10.1186/1471-2350-9-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 02/07/2008] [Indexed: 01/23/2023]
Abstract
Background Whole genome amplification (WGA) methods allow diagnostic laboratories to overcome the common problem of insufficient DNA in patient specimens. Further, body fluid samples useful for cancer early detection are often difficult to amplify with traditional PCR methods. In this first application of WGA on the entire human mitochondrial genome, we compared the accuracy of mitochondrial DNA (mtDNA) sequence analysis after WGA to that performed without genome amplification. We applied the method to a small group of cancer cases and controls and demonstrated that WGA is capable of increasing the yield of starting DNA material with identical genetic sequence. Methods DNA was isolated from clinical samples and sent to NIST. Samples were amplified by PCR and those with no visible amplification were re-amplified using the Multiple Displacement Amplificaiton technique of whole genome amplification. All samples were analyzed by mitochip for mitochondrial DNA sequence to compare sequence concordance of the WGA samples with respect to native DNA. Real-Time PCR analysis was conducted to determine the level of WGA amplification for both nuclear and mtDNA. Results In total, 19 samples were compared and the concordance rate between WGA and native mtDNA sequences was 99.995%. All of the cancer associated mutations in the native mtDNA were detected in the WGA amplified material and heteroplasmies in the native mtDNA were detected with high fidelity in the WGA material. In addition to the native mtDNA sequence present in the sample, 13 new heteroplasmies were detected in the WGA material. Conclusion Genetic screening of mtDNA amplified by WGA is applicable for the detection of cancer associated mutations. Our results show the feasibility of this method for: 1) increasing the amount of DNA available for analysis, 2) recovering the identical mtDNA sequence, 3) accurately detecting mtDNA point mutations associated with cancer.
Collapse
Affiliation(s)
- Samantha Maragh
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
| | | | | | | | | | | | | |
Collapse
|
27
|
Nørgaard-Pedersen B, Hougaard DM. Storage policies and use of the Danish Newborn Screening Biobank. J Inherit Metab Dis 2007; 30:530-6. [PMID: 17632694 DOI: 10.1007/s10545-007-0631-x] [Citation(s) in RCA: 177] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 03/15/2007] [Accepted: 05/31/2007] [Indexed: 01/13/2023]
Abstract
After routine newborn screening, residual dried blood spot samples (DBSS) are stored at -20 degrees C in the Danish Newborn Screening Biobank (NBS-Biobank), which contains DBSS from virtually all newborns in Denmark since 1982--about 1.8 million samples. The purpose of the storage is: (1) diagnosis and treatment of congenital disorders including documentation, repeat testing, quality assurance, statistics and improvement of screening methods; (2) diagnostic use later in infancy after informed consent; (3) legal use after court order; (4) the possibility of research projects after approval by the Scientific Ethical Committee System in Denmark, The Danish Data Protection Agency and the NBS-Biobank Steering Committee. The operation and use of the NBS-Biobank has until recently been regulated by an executive order of 1993 from the Danish Ministry of Health. The Ethical Council, the Central Scientific Ethical Committee and the National Board of Health were also involved in the regulations. These regulations have now been replaced by detailed general operational guidelines for biobanks in Denmark according to Acts on Processing of Personal Data, Patient's Rights, Health 546/2005 and the Biomedical Research Ethics Committee System. No specific Act on biobanks per se has been made in Denmark, but the new regulations and guidelines make the operations of the Danish NBS-Biobank even more clear-cut and safe. The Danish NBS-Biobank has been used in several research projects for aetiological studies of a number of disorders, recently employing new sensitive multiplex technologies and genetic analyses utilizing whole-genome amplified DNA.
Collapse
Affiliation(s)
- B Nørgaard-Pedersen
- Department of Clinical Biochemistry, Statens Serum Institut, Copenhagen, Denmark.
| | | |
Collapse
|
28
|
Production of in vitro amplified DNA pseudolibraries and high-throughput cDNA target amplification. BMC Biotechnol 2007; 7:31. [PMID: 17565673 PMCID: PMC1894961 DOI: 10.1186/1472-6750-7-31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 06/12/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many structural biology- and high-throughput laboratories experience the acquisition of multiple cDNAs from different sources as a rather time- and resource-consuming procedure. The techniques presented here solve these problems. RESULTS An advanced target cDNA amplification procedure employing RNA- or cDNA-derived pseudolibraries circumvents the usual DNA transfection during library establishment. A small sample of reverse transcribed ss- or ds-cDNA or DNA from a pre-existing library is multiplied by in vitro rolling circle ramification amplification. The resulting cDNA pseudolibrary serves as a template for numerous highly efficient PCR amplifications and permits production and analysis of target cDNAs on an automated liquid handling workstation. CONCLUSION The overall efficiency of the simple protocol collection approaches 100% for targets from libraries with low complexity such as Drosophila and yields >80% of amplicons up to 3 kb size in the case of human cDNA.
Collapse
|